Starting phenix.real_space_refine on Fri Mar 22 21:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut1_42526/03_2024/8ut1_42526_trim_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 115 5.16 5 Cl 5 4.86 5 C 11345 2.51 5 N 2630 2.21 5 O 3180 1.98 5 H 15845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33140 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6345 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6417 Chain: "B" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6345 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6417 Chain: "C" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6345 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6417 Chain: "D" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6345 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6417 Chain: "E" Number of atoms: 6357 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6344 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6345 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6417 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 195 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 24.55, per 1000 atoms: 0.74 Number of scatterers: 33140 At special positions: 0 Unit cell: (98.189, 102.505, 167.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 115 16.00 P 15 15.00 O 3180 8.00 N 2630 7.00 C 11345 6.00 H 15845 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 603 " - " ASN B 67 " " NAG C 603 " - " ASN C 67 " " NAG D 603 " - " ASN D 67 " " NAG E 603 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 24.31 Conformation dependent library (CDL) restraints added in 5.9 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 25 sheets defined 40.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.506A pdb=" N ALA A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.510A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 409 through 466 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.506A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.509A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.506A pdb=" N ALA C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.510A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.506A pdb=" N ALA D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 238 through 258 removed outlier: 3.509A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 removed outlier: 3.506A pdb=" N ALA E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.510A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 295 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.377A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.482A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.377A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.482A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.376A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.482A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.377A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.481A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.376A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.482A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.71 Time building geometry restraints manager: 25.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15810 1.04 - 1.24: 2183 1.24 - 1.44: 5334 1.44 - 1.64: 10063 1.64 - 1.84: 175 Bond restraints: 33565 Sorted by residual: bond pdb=" C3 EPJ E 607 " pdb=" N1 EPJ E 607 " ideal model delta sigma weight residual 1.718 1.464 0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C3 EPJ B 607 " pdb=" N1 EPJ B 607 " ideal model delta sigma weight residual 1.718 1.464 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C3 EPJ A 606 " pdb=" N1 EPJ A 606 " ideal model delta sigma weight residual 1.718 1.464 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C3 EPJ C 607 " pdb=" N1 EPJ C 607 " ideal model delta sigma weight residual 1.718 1.464 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C3 EPJ D 607 " pdb=" N1 EPJ D 607 " ideal model delta sigma weight residual 1.718 1.464 0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 33560 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.37: 230 103.37 - 111.05: 34381 111.05 - 118.72: 10680 118.72 - 126.39: 14363 126.39 - 134.07: 441 Bond angle restraints: 60095 Sorted by residual: angle pdb=" C4 EPJ E 607 " pdb=" C3 EPJ E 607 " pdb=" N1 EPJ E 607 " ideal model delta sigma weight residual 93.85 103.45 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C4 EPJ B 607 " pdb=" C3 EPJ B 607 " pdb=" N1 EPJ B 607 " ideal model delta sigma weight residual 93.85 103.43 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C4 EPJ A 606 " pdb=" C3 EPJ A 606 " pdb=" N1 EPJ A 606 " ideal model delta sigma weight residual 93.85 103.42 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C4 EPJ C 607 " pdb=" C3 EPJ C 607 " pdb=" N1 EPJ C 607 " ideal model delta sigma weight residual 93.85 103.40 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C4 EPJ D 607 " pdb=" C3 EPJ D 607 " pdb=" N1 EPJ D 607 " ideal model delta sigma weight residual 93.85 103.40 -9.55 3.00e+00 1.11e-01 1.01e+01 ... (remaining 60090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 16215 31.05 - 62.11: 540 62.11 - 93.16: 100 93.16 - 124.21: 35 124.21 - 155.26: 25 Dihedral angle restraints: 16915 sinusoidal: 9740 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 16912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2211 0.056 - 0.111: 386 0.111 - 0.167: 123 0.167 - 0.222: 10 0.222 - 0.278: 10 Chirality restraints: 2740 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.25e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.23e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.23e+01 ... (remaining 2737 not shown) Planarity restraints: 4735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 78 " -0.295 9.50e-02 1.11e+02 1.04e-01 3.53e+01 pdb=" NE ARG C 78 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 78 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG C 78 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 78 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 78 " 0.061 2.00e-02 2.50e+03 pdb="HH12 ARG C 78 " -0.023 2.00e-02 2.50e+03 pdb="HH21 ARG C 78 " 0.055 2.00e-02 2.50e+03 pdb="HH22 ARG C 78 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 78 " 0.295 9.50e-02 1.11e+02 1.04e-01 3.53e+01 pdb=" NE ARG B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 78 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG B 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 78 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 78 " -0.061 2.00e-02 2.50e+03 pdb="HH12 ARG B 78 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG B 78 " -0.055 2.00e-02 2.50e+03 pdb="HH22 ARG B 78 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 78 " 0.294 9.50e-02 1.11e+02 1.04e-01 3.51e+01 pdb=" NE ARG A 78 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 78 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 78 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 78 " -0.061 2.00e-02 2.50e+03 pdb="HH12 ARG A 78 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG A 78 " -0.055 2.00e-02 2.50e+03 pdb="HH22 ARG A 78 " 0.024 2.00e-02 2.50e+03 ... (remaining 4732 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 707 2.13 - 2.75: 57721 2.75 - 3.37: 91586 3.37 - 3.98: 124303 3.98 - 4.60: 189371 Nonbonded interactions: 463688 Sorted by model distance: nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.513 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.514 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.514 2.100 ... (remaining 463683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 478 or resid 604)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478 or (resid 604 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or n \ ame O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P or \ name C210 or name C211)))) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.490 Extract box with map and model: 5.160 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 110.170 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.254 17715 Z= 0.626 Angle : 0.851 9.597 24075 Z= 0.386 Chirality : 0.050 0.278 2740 Planarity : 0.007 0.110 2855 Dihedral : 19.183 155.263 7540 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.56 % Allowed : 0.00 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 1955 helix: 1.11 (0.18), residues: 800 sheet: -0.75 (0.23), residues: 440 loop : -0.34 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 307 HIS 0.002 0.001 HIS D 140 PHE 0.020 0.001 PHE C 99 TYR 0.014 0.002 TYR D 117 ARG 0.034 0.002 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 350 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8343 (mtp) cc_final: 0.7936 (mtp) REVERT: B 188 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7669 (mp0) REVERT: B 258 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 446 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8119 (tpp80) REVERT: C 252 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7533 (t80) REVERT: C 260 MET cc_start: 0.8974 (mmm) cc_final: 0.8548 (mmm) REVERT: C 322 MET cc_start: 0.8345 (mtp) cc_final: 0.8098 (mtp) REVERT: C 446 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8127 (tpp80) REVERT: D 40 MET cc_start: 0.8514 (mtp) cc_final: 0.8099 (mtp) REVERT: D 446 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8075 (tpp80) REVERT: E 57 MET cc_start: 0.9051 (mtm) cc_final: 0.8845 (mtp) REVERT: E 188 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 260 MET cc_start: 0.9035 (mmm) cc_final: 0.8781 (mmm) REVERT: E 446 ARG cc_start: 0.8250 (tpp80) cc_final: 0.8003 (tpp80) outliers start: 10 outliers final: 6 residues processed: 360 average time/residue: 2.4668 time to fit residues: 1001.2665 Evaluate side-chains 276 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 269 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0970 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 213 ASN B 427 GLN ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 293 GLN D 213 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17715 Z= 0.178 Angle : 0.578 6.152 24075 Z= 0.290 Chirality : 0.040 0.147 2740 Planarity : 0.004 0.037 2855 Dihedral : 18.048 150.303 3789 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.06 % Allowed : 8.29 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1955 helix: 1.92 (0.18), residues: 800 sheet: -0.48 (0.23), residues: 445 loop : -0.04 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.002 0.000 HIS B 295 PHE 0.010 0.001 PHE A 99 TYR 0.011 0.001 TYR E 294 ARG 0.005 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 57 MET cc_start: 0.9065 (mtm) cc_final: 0.8854 (mtp) REVERT: B 188 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7676 (mp0) REVERT: B 258 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6479 (mm-30) REVERT: C 252 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7545 (t80) REVERT: C 258 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6462 (mm-30) REVERT: C 260 MET cc_start: 0.8967 (mmm) cc_final: 0.8547 (mmm) REVERT: C 322 MET cc_start: 0.8288 (mtp) cc_final: 0.8080 (mtp) REVERT: C 446 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7805 (tpp80) REVERT: D 40 MET cc_start: 0.8562 (mtp) cc_final: 0.8105 (mtp) REVERT: D 265 ASP cc_start: 0.8298 (m-30) cc_final: 0.8089 (m-30) REVERT: D 430 SER cc_start: 0.8592 (t) cc_final: 0.8386 (m) REVERT: D 450 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6745 (mpm) REVERT: E 57 MET cc_start: 0.9058 (mtm) cc_final: 0.8843 (mtp) REVERT: E 188 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7532 (mm-30) REVERT: E 260 MET cc_start: 0.9020 (mmm) cc_final: 0.8770 (mmm) REVERT: E 278 MET cc_start: 0.7371 (tpt) cc_final: 0.7169 (mmt) outliers start: 19 outliers final: 8 residues processed: 294 average time/residue: 2.1829 time to fit residues: 734.9725 Evaluate side-chains 276 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17715 Z= 0.208 Angle : 0.566 5.906 24075 Z= 0.287 Chirality : 0.040 0.150 2740 Planarity : 0.005 0.050 2855 Dihedral : 15.601 144.607 3787 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.90 % Allowed : 9.64 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1955 helix: 2.25 (0.18), residues: 800 sheet: -0.36 (0.23), residues: 445 loop : 0.16 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 148 HIS 0.003 0.001 HIS D 297 PHE 0.017 0.001 PHE E 319 TYR 0.012 0.002 TYR D 14 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 270 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 MET cc_start: 0.7145 (mtt) cc_final: 0.6861 (mtt) REVERT: C 252 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7495 (t80) REVERT: C 258 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6385 (mm-30) REVERT: C 260 MET cc_start: 0.8948 (mmm) cc_final: 0.8643 (mmm) REVERT: C 322 MET cc_start: 0.8312 (mtp) cc_final: 0.8100 (mtp) REVERT: C 446 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7837 (tpp80) REVERT: D 40 MET cc_start: 0.8608 (mtp) cc_final: 0.8235 (mtp) REVERT: D 430 SER cc_start: 0.8729 (t) cc_final: 0.8508 (m) REVERT: D 450 MET cc_start: 0.6917 (mmt) cc_final: 0.6586 (mpm) REVERT: E 57 MET cc_start: 0.9064 (mtm) cc_final: 0.8704 (mtp) REVERT: E 188 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 260 MET cc_start: 0.9036 (mmm) cc_final: 0.8806 (mmm) outliers start: 16 outliers final: 9 residues processed: 277 average time/residue: 2.1655 time to fit residues: 688.9620 Evaluate side-chains 267 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17715 Z= 0.172 Angle : 0.509 6.786 24075 Z= 0.263 Chirality : 0.038 0.146 2740 Planarity : 0.004 0.040 2855 Dihedral : 14.479 138.850 3787 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.23 % Allowed : 10.42 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1955 helix: 2.46 (0.17), residues: 800 sheet: -0.33 (0.23), residues: 445 loop : 0.21 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 173 HIS 0.002 0.001 HIS E 295 PHE 0.018 0.001 PHE E 319 TYR 0.009 0.001 TYR C 14 ARG 0.006 0.001 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 267 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7448 (t80) REVERT: C 258 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6321 (mm-30) REVERT: C 260 MET cc_start: 0.8932 (mmm) cc_final: 0.8551 (mmm) REVERT: C 278 MET cc_start: 0.7616 (mmm) cc_final: 0.7408 (mmm) REVERT: C 446 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7805 (tpp80) REVERT: D 40 MET cc_start: 0.8582 (mtp) cc_final: 0.8206 (mtp) REVERT: D 450 MET cc_start: 0.6805 (mmt) cc_final: 0.6570 (mpm) REVERT: E 57 MET cc_start: 0.9068 (mtm) cc_final: 0.8677 (mtp) REVERT: E 188 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7573 (mm-30) REVERT: E 260 MET cc_start: 0.9033 (mmm) cc_final: 0.8798 (mmm) outliers start: 22 outliers final: 10 residues processed: 277 average time/residue: 2.1792 time to fit residues: 693.8438 Evaluate side-chains 273 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 169 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17715 Z= 0.146 Angle : 0.481 5.453 24075 Z= 0.247 Chirality : 0.038 0.143 2740 Planarity : 0.004 0.037 2855 Dihedral : 13.536 132.138 3787 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.73 % Allowed : 11.43 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 1955 helix: 2.68 (0.17), residues: 800 sheet: -0.31 (0.23), residues: 445 loop : 0.31 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 85 HIS 0.002 0.000 HIS D 295 PHE 0.018 0.001 PHE E 319 TYR 0.008 0.001 TYR C 14 ARG 0.005 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 263 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7471 (t80) REVERT: C 258 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6214 (mm-30) REVERT: C 260 MET cc_start: 0.8921 (mmm) cc_final: 0.8531 (mmm) REVERT: C 435 SER cc_start: 0.8393 (m) cc_final: 0.8151 (p) REVERT: C 446 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7807 (tpp80) REVERT: D 40 MET cc_start: 0.8564 (mtp) cc_final: 0.8181 (mtp) REVERT: D 450 MET cc_start: 0.6755 (mmt) cc_final: 0.6513 (mpm) REVERT: E 40 MET cc_start: 0.8568 (mtp) cc_final: 0.8281 (mtp) REVERT: E 57 MET cc_start: 0.9056 (mtm) cc_final: 0.8772 (mtp) REVERT: E 188 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7567 (mm-30) REVERT: E 260 MET cc_start: 0.9020 (mmm) cc_final: 0.8780 (mmm) outliers start: 13 outliers final: 11 residues processed: 273 average time/residue: 2.0978 time to fit residues: 658.6935 Evaluate side-chains 267 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 255 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17715 Z= 0.261 Angle : 0.554 5.121 24075 Z= 0.289 Chirality : 0.040 0.159 2740 Planarity : 0.005 0.060 2855 Dihedral : 13.518 130.138 3787 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.90 % Allowed : 11.15 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1955 helix: 2.65 (0.17), residues: 800 sheet: -0.32 (0.23), residues: 445 loop : 0.26 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 173 HIS 0.003 0.001 HIS A 140 PHE 0.018 0.002 PHE E 319 TYR 0.014 0.002 TYR E 31 ARG 0.009 0.001 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 SER cc_start: 0.8594 (m) cc_final: 0.8338 (p) REVERT: C 252 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7476 (t80) REVERT: C 258 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6264 (mm-30) REVERT: C 260 MET cc_start: 0.8919 (mmm) cc_final: 0.8554 (mmm) REVERT: C 322 MET cc_start: 0.8308 (mtp) cc_final: 0.8085 (mtp) REVERT: C 435 SER cc_start: 0.8412 (m) cc_final: 0.8165 (p) REVERT: D 40 MET cc_start: 0.8613 (mtp) cc_final: 0.8265 (mtp) REVERT: D 450 MET cc_start: 0.6829 (mmt) cc_final: 0.6583 (mpm) REVERT: E 57 MET cc_start: 0.9095 (mtm) cc_final: 0.8785 (mtp) outliers start: 16 outliers final: 9 residues processed: 282 average time/residue: 2.1534 time to fit residues: 706.0969 Evaluate side-chains 270 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17715 Z= 0.201 Angle : 0.520 4.386 24075 Z= 0.271 Chirality : 0.039 0.154 2740 Planarity : 0.004 0.041 2855 Dihedral : 13.251 128.681 3787 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.84 % Allowed : 11.54 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1955 helix: 2.67 (0.17), residues: 800 sheet: -0.34 (0.23), residues: 445 loop : 0.24 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 173 HIS 0.002 0.001 HIS A 140 PHE 0.019 0.001 PHE E 319 TYR 0.010 0.001 TYR C 14 ARG 0.008 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 SER cc_start: 0.8572 (m) cc_final: 0.8345 (p) REVERT: C 252 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7430 (t80) REVERT: C 258 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6304 (mm-30) REVERT: C 260 MET cc_start: 0.8911 (mmm) cc_final: 0.8497 (mmm) REVERT: C 435 SER cc_start: 0.8389 (m) cc_final: 0.8176 (p) REVERT: D 40 MET cc_start: 0.8594 (mtp) cc_final: 0.8248 (mtp) REVERT: D 450 MET cc_start: 0.6818 (mmt) cc_final: 0.6574 (mpm) REVERT: E 57 MET cc_start: 0.9099 (mtm) cc_final: 0.8798 (mtp) outliers start: 15 outliers final: 12 residues processed: 276 average time/residue: 2.1203 time to fit residues: 672.6722 Evaluate side-chains 274 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 261 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17715 Z= 0.204 Angle : 0.520 4.719 24075 Z= 0.271 Chirality : 0.039 0.156 2740 Planarity : 0.004 0.041 2855 Dihedral : 13.056 126.430 3787 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.95 % Allowed : 11.48 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 1955 helix: 2.74 (0.17), residues: 800 sheet: -0.34 (0.23), residues: 445 loop : 0.24 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 173 HIS 0.002 0.001 HIS A 140 PHE 0.019 0.001 PHE E 319 TYR 0.011 0.001 TYR D 14 ARG 0.006 0.001 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 265 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 SER cc_start: 0.8569 (m) cc_final: 0.8344 (p) REVERT: C 252 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7432 (t80) REVERT: C 258 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6252 (mm-30) REVERT: C 260 MET cc_start: 0.8884 (mmm) cc_final: 0.8631 (mmm) REVERT: D 40 MET cc_start: 0.8587 (mtp) cc_final: 0.8248 (mtp) REVERT: D 450 MET cc_start: 0.6809 (mmt) cc_final: 0.6565 (mpm) REVERT: E 57 MET cc_start: 0.9096 (mtm) cc_final: 0.8871 (mtp) outliers start: 17 outliers final: 13 residues processed: 276 average time/residue: 2.1206 time to fit residues: 673.8323 Evaluate side-chains 275 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17715 Z= 0.143 Angle : 0.477 5.246 24075 Z= 0.247 Chirality : 0.038 0.143 2740 Planarity : 0.004 0.040 2855 Dihedral : 12.559 124.813 3787 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.62 % Allowed : 11.88 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 1955 helix: 2.84 (0.17), residues: 800 sheet: -0.34 (0.23), residues: 445 loop : 0.32 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 85 HIS 0.002 0.000 HIS A 140 PHE 0.020 0.001 PHE E 319 TYR 0.008 0.001 TYR C 14 ARG 0.006 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 265 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7392 (t80) REVERT: C 258 GLU cc_start: 0.6553 (mm-30) cc_final: 0.6318 (mm-30) REVERT: C 260 MET cc_start: 0.8868 (mmm) cc_final: 0.8623 (mmm) REVERT: D 40 MET cc_start: 0.8544 (mtp) cc_final: 0.8211 (mtp) REVERT: D 450 MET cc_start: 0.6801 (mmt) cc_final: 0.6558 (mpm) REVERT: E 57 MET cc_start: 0.9077 (mtm) cc_final: 0.8769 (mtp) outliers start: 11 outliers final: 9 residues processed: 274 average time/residue: 2.0998 time to fit residues: 662.4462 Evaluate side-chains 271 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17715 Z= 0.158 Angle : 0.484 5.251 24075 Z= 0.251 Chirality : 0.038 0.145 2740 Planarity : 0.004 0.038 2855 Dihedral : 12.323 124.159 3787 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.62 % Allowed : 12.04 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1955 helix: 2.90 (0.17), residues: 800 sheet: -0.34 (0.23), residues: 445 loop : 0.35 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 85 HIS 0.002 0.001 HIS A 140 PHE 0.020 0.001 PHE E 319 TYR 0.008 0.001 TYR C 14 ARG 0.006 0.000 ARG D 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7416 (t80) REVERT: C 258 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6309 (mm-30) REVERT: C 260 MET cc_start: 0.8858 (mmm) cc_final: 0.8606 (mmm) REVERT: D 40 MET cc_start: 0.8551 (mtp) cc_final: 0.8218 (mtp) REVERT: D 309 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7955 (ttm-80) REVERT: D 450 MET cc_start: 0.6771 (mmt) cc_final: 0.6535 (mpm) REVERT: E 57 MET cc_start: 0.9077 (mtm) cc_final: 0.8766 (mtp) outliers start: 11 outliers final: 10 residues processed: 271 average time/residue: 2.1355 time to fit residues: 666.4842 Evaluate side-chains 271 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.4980 chunk 47 optimal weight: 0.0370 chunk 142 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.0170 chunk 136 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099155 restraints weight = 55695.918| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.76 r_work: 0.2902 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17715 Z= 0.127 Angle : 0.459 5.054 24075 Z= 0.236 Chirality : 0.037 0.140 2740 Planarity : 0.004 0.040 2855 Dihedral : 11.883 124.674 3787 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.50 % Allowed : 11.99 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 1955 helix: 2.96 (0.17), residues: 800 sheet: -0.35 (0.23), residues: 445 loop : 0.38 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.001 0.000 HIS A 295 PHE 0.019 0.001 PHE E 319 TYR 0.007 0.001 TYR A 117 ARG 0.006 0.000 ARG D 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12109.48 seconds wall clock time: 211 minutes 50.64 seconds (12710.64 seconds total)